Variant report

Variant	rs3797776
Chromosome Location	chr5:179193598-179193599
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

TF binding
region (count:32)
CpG islands
(count:0)
Chromatin interactive
region (count:19)
LncRNA
region (count:0)
Mature miRNA
region (count: 0)
miRNA target
sites (count:0)

(count:32 , 50 per page) page: 1

No.	Transcrition factor	Chromosome Location	Cell Line	Cell type	Cell Stage	Matched TF binding sites
1	BHLHE40	chr5:179193441-179193907	K562	blood:	n/a	n/a
2	CCNT2	chr5:179193496-179193788	K562	blood:	n/a	n/a
3	MAX	chr5:179193217-179193647	NB4	blood:	n/a	n/a
4	MAX	chr5:179193233-179193823	K562	blood:	n/a	n/a
5	MYC	chr5:179193340-179193674	NB4	blood:	n/a	n/a
6	EP300	chr5:179193442-179193791	K562	blood:	n/a	n/a
7	TEAD4	chr5:179193480-179193894	K562	blood:	n/a	n/a
8	MAFK	chr5:179193335-179193627	IMR90	lung:	n/a	n/a
9	MAX	chr5:179193462-179193756	K562	blood:	n/a	n/a
10	POLR2A	chr5:179193384-179193788	K562	blood:	n/a	n/a
11	MAZ	chr5:179193411-179193702	K562	blood:	n/a	n/a
12	GATA1	chr5:179193345-179194320	PBDE	blood:	n/a	chr5:179194046-179194063
13	JUND	chr5:179193370-179193762	K562	blood:	n/a	n/a
14	TAL1	chr5:179193452-179193846	K562	blood:	n/a	n/a
15	ARID3A	chr5:179193473-179193721	K562	blood:	n/a	n/a
16	TEAD4	chr5:179193409-179193909	K562	blood:	n/a	n/a
17	FOSL2	chr5:179193167-179193797	SK-N-SH	brain:	n/a	n/a
18	RCOR1	chr5:179193405-179193800	K562	blood:	n/a	n/a
19	UBTF	chr5:179193459-179193744	K562	blood:	n/a	n/a
20	RCOR1	chr5:179193463-179193680	K562	blood:	n/a	n/a
21	POLR2A	chr5:179191688-179193979	K562	blood:	n/a	n/a
22	CUX1	chr5:179193472-179193907	K562	blood:	n/a	n/a
23	ZNF143	chr5:179193587-179193778	K562	blood:	n/a	n/a
24	ZBTB7A	chr5:179193356-179193667	K562	blood:	n/a	n/a
25	MYC	chr5:179193364-179193819	K562	blood:	n/a	n/a
26	TBL1XR1	chr5:179193569-179193761	K562	blood:	n/a	n/a
27	TCF12	chr5:179191917-179193796	SK-N-SH	brain:	n/a	n/a
28	MAX	chr5:179193232-179193699	SK-N-SH	brain:	n/a	n/a
29	FOS	chr5:179193560-179193752	MCF10A-Er-Src	breast:	n/a	n/a
30	MAFF	chr5:179193321-179193674	K562	blood:	n/a	n/a
31	JUN	chr5:179193359-179193763	K562	blood:	n/a	n/a
32	MAFK	chr5:179193335-179193797	K562	blood:	n/a	n/a

No data

(count:19 , 50 per page) page: 1

No.	Distal block	Cell Line	Cell type
1	chr5:179193094..179194973-chr5:179497469..179499850,2	K562	blood:
2	chr5:179192837..179195567-chr5:179212671..179216209,3	K562	blood:
3	chr5:179183483..179185130-chr5:179191548..179193650,2	K562	blood:
4	chr5:179191220..179194008-chr5:179228937..179231114,2	K562	blood:
5	chr1:149223887..149224483-chr5:179193253..179194234,3	MCF-7	breast:
6	chr5:179192355..179194197-chr5:179212856..179215229,2	MCF-7	breast:
7	chr5:179192926..179195030-chr5:179200613..179202484,2	MCF-7	breast:
8	chr5:179159859..179161740-chr5:179192124..179194566,2	MCF-7	breast:
9	chr1:149223298..149225446-chr5:179192233..179193754,3	MCF-7	breast:
10	chr5:179189180..179191928-chr5:179192012..179195048,3	K562	blood:
11	chr1:149223791..149225452-chr5:179192234..179193753,4	MCF-7	breast:
12	chr5:179183781..179185717-chr5:179193398..179195095,2	K562	blood:
13	chr5:179190740..179195492-chr5:179198923..179204539,8	MCF-7	breast:
14	chr5:179192430..179194832-chr5:179221034..179223075,2	MCF-7	breast:
15	chr5:179190822..179197512-chr5:179244986..179249382,7	K562	blood:
16	chr5:179173901..179176407-chr5:179192308..179193832,2	MCF-7	breast:
17	chr5:179192485..179195191-chr5:179221488..179224022,4	MCF-7	breast:
18	chr5:179192680..179196164-chr5:179217971..179221244,3	MCF-7	breast:
19	chr5:179186999..179190414-chr5:179192166..179194492,3	MCF-7	breast:

No data

Variant related genes	Relation type
MAML1	TF binding region
ENSG00000161021	Chromatin interaction
ENSG00000113269	Chromatin interaction
ENSG00000213316	Chromatin interaction
ENSG00000161013	Chromatin interaction
ENSG00000161011	Chromatin interaction
ENSG00000206737	Chromatin interaction

Extended variants
information (count: 62 )
Associated
traits (count: 4 )

rSNPs within LD-proxies of this variant (count:53)

rs_ID	r²[population]
rs11738269	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.96[MKK][hapmap];1.00[TSI][hapmap];0.98[AMR][1000 genomes];0.94[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11738720	1.00[CHB][hapmap];0.93[CHD][hapmap];0.92[JPT][hapmap];0.81[AMR][1000 genomes];0.80[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs11739042	0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11740569	0.91[AMR][1000 genomes];0.91[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs11741570	0.97[AMR][1000 genomes];0.94[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11743232	0.84[ASN][1000 genomes]
rs11744616	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.94[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11746924	0.92[AMR][1000 genomes];0.91[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs11747496	0.94[AMR][1000 genomes];0.89[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs12522263	0.84[AMR][1000 genomes];0.83[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs1469020	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.85[AFR][1000 genomes];0.97[AMR][1000 genomes];0.89[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs1469021	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[LWK][hapmap];0.94[MEX][hapmap];1.00[MKK][hapmap];0.97[TSI][hapmap];1.00[AFR][1000 genomes];0.97[AMR][1000 genomes];0.89[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs17617068	1.00[CEU][hapmap];1.00[CHB][hapmap];0.93[CHD][hapmap];0.87[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];0.96[MKK][hapmap];0.97[TSI][hapmap];0.94[AMR][1000 genomes];0.93[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs17617710	1.00[CHB][hapmap];1.00[CHD][hapmap];0.94[GIH][hapmap];1.00[JPT][hapmap];0.81[AMR][1000 genomes];0.85[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs34057110	0.88[ASN][1000 genomes]
rs3756614	0.94[ASN][1000 genomes]
rs3797762	1.00[CHB][hapmap];1.00[CHD][hapmap];0.94[GIH][hapmap];0.92[JPT][hapmap];0.81[AMR][1000 genomes];0.86[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs41458244	0.84[AFR][1000 genomes];0.92[AMR][1000 genomes];0.84[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs4700838	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];0.92[MKK][hapmap];1.00[TSI][hapmap];0.97[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4700840	1.00[AFR][1000 genomes];0.97[AMR][1000 genomes];0.98[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs55654737	0.97[ASN][1000 genomes]
rs55827522	0.98[AMR][1000 genomes];0.93[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs55975622	0.94[AMR][1000 genomes];0.93[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs56309143	0.94[AMR][1000 genomes];0.89[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs56335144	0.97[AMR][1000 genomes];0.93[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs58386410	0.81[AMR][1000 genomes];0.85[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs62404347	0.81[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs62406176	0.92[AMR][1000 genomes];0.93[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs62406177	0.94[AMR][1000 genomes];0.93[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs62406178	0.95[AMR][1000 genomes];0.93[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs62406181	0.81[AMR][1000 genomes];0.83[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs62406187	0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs62406219	0.95[AMR][1000 genomes];0.93[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs62406223	0.91[AMR][1000 genomes];0.83[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs62406227	0.81[AMR][1000 genomes]
rs62406228	0.83[AMR][1000 genomes]
rs6601067	0.89[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs6601072	0.94[AMR][1000 genomes];0.93[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs6639	1.00[CHB][hapmap];0.93[CHD][hapmap];0.92[JPT][hapmap];0.81[AMR][1000 genomes];0.82[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs6860716	0.81[AMR][1000 genomes];0.83[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs6887507	0.81[AMR][1000 genomes];0.89[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6893300	1.00[CEU][hapmap];1.00[CHB][hapmap];0.93[CHD][hapmap];0.83[GIH][hapmap];0.92[JPT][hapmap];0.94[MEX][hapmap];0.94[TSI][hapmap];0.81[AMR][1000 genomes];0.89[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs6895902	1.00[CHB][hapmap];1.00[CHD][hapmap];0.94[GIH][hapmap];1.00[JPT][hapmap];0.81[AMR][1000 genomes];0.87[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs72807339	0.86[AMR][1000 genomes];0.82[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs730012	1.00[CEU][hapmap];0.91[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];0.92[JPT][hapmap];0.81[MEX][hapmap];0.97[TSI][hapmap];0.91[AMR][1000 genomes];0.83[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs7444006	1.00[CHB][hapmap];0.97[AMR][1000 genomes];0.92[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs7447159	0.97[AMR][1000 genomes];0.93[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs7704520	1.00[CHB][hapmap];1.00[JPT][hapmap];0.81[AMR][1000 genomes];0.89[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7705530	1.00[CHB][hapmap];1.00[JPT][hapmap];0.81[AMR][1000 genomes];0.89[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7709723	0.81[CHB][hapmap];0.93[CHD][hapmap]
rs7715356	1.00[CHB][hapmap];0.93[CHD][hapmap];0.92[JPT][hapmap];0.80[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs7734102	1.00[CHB][hapmap];0.93[CHD][hapmap];0.92[JPT][hapmap];0.81[AMR][1000 genomes];0.81[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs7735702	1.00[CEU][hapmap];1.00[CHB][hapmap];0.92[JPT][hapmap];0.81[AMR][1000 genomes];0.89[EUR][1000 genomes];0.86[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:9 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv949554	chr5:178832325-179309513	Transcr. at gene 5' and 3' Weak transcription Strong transcription Active TSS Enhancers Genic enhancers ZNF genes & repeats Flanking Active TSS Bivalent/Poised TSS Flanking Bivalent TSS/Enh Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	312 gene(s)	inside rSNPs	diseases
2	nsv883270	chr5:178951106-179350387	Weak transcription Strong transcription Flanking Active TSS Enhancers Genic enhancers Active TSS Transcr. at gene 5' and 3' ZNF genes & repeats Bivalent/Poised TSS Flanking Bivalent TSS/Enh Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	312 gene(s)	inside rSNPs	diseases
3	nsv531997	chr5:179107599-179588082	Enhancers Strong transcription Flanking Active TSS ZNF genes & repeats Weak transcription Genic enhancers Flanking Bivalent TSS/Enh Active TSS Bivalent/Poised TSS Transcr. at gene 5' and 3' Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	339 gene(s)	inside rSNPs	diseases
4	nsv469579	chr5:179184831-179360191	Genic enhancers Active TSS Weak transcription Enhancers Flanking Active TSS Strong transcription Bivalent/Poised TSS ZNF genes & repeats Bivalent Enhancer Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	182 gene(s)	inside rSNPs	diseases
5	nsv883274	chr5:179186397-179310330	Strong transcription Weak transcription Enhancers ZNF genes & repeats Flanking Active TSS Transcr. at gene 5' and 3' Active TSS Genic enhancers Flanking Bivalent TSS/Enh Bivalent/Poised TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	178 gene(s)	inside rSNPs	diseases
6	nsv518964	chr5:179193598-179227286	Strong transcription Enhancers Active TSS Weak transcription Genic enhancers ZNF genes & repeats Flanking Active TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Bivalent Enhancer Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	151 gene(s)	inside rSNPs	diseases
7	nsv883275	chr5:179193598-179267783	Weak transcription Flanking Active TSS Flanking Bivalent TSS/Enh Genic enhancers Enhancers Active TSS Strong transcription Bivalent/Poised TSS Transcr. at gene 5' and 3' ZNF genes & repeats Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	176 gene(s)	inside rSNPs	diseases
8	nsv883276	chr5:179193598-179310330	Flanking Active TSS Strong transcription Weak transcription ZNF genes & repeats Genic enhancers Enhancers Active TSS Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent/Poised TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	178 gene(s)	inside rSNPs	diseases
9	nsv883277	chr5:179193598-179350387	Genic enhancers Enhancers Weak transcription Flanking Active TSS Strong transcription Transcr. at gene 5' and 3' ZNF genes & repeats Active TSS Flanking Bivalent TSS/Enh Bivalent Enhancer Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	182 gene(s)	inside rSNPs	diseases

mRNA abundance (count:4)

SNP	Gene	Cis/trans	Tissue	Source
rs3797776	CANX	cis	cerebellum	SCAN
rs3797776	CANX	cis	parietal	SCAN
rs3797776	C5orf45	cis	parietal	SCAN
rs3797776	TRIM52	cis	parietal	SCAN

Chromatin state (count:127 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr5:179188600-179193600	Enhancers	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
2	chr5:179188800-179193600	Enhancers	ES-I3 Cell Line	embryonic stem cell
3	chr5:179189800-179194000	Weak transcription	Pancreatic Islets	Pancreatic Islet
4	chr5:179190600-179194800	Enhancers	Right Atrium	heart
5	chr5:179190800-179207600	Strong transcription	Dnd41	blood
6	chr5:179191000-179193800	Genic enhancers	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
7	chr5:179191000-179203000	Weak transcription	Psoas Muscle	Psoas
8	chr5:179191200-179195400	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
9	chr5:179191200-179196000	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
10	chr5:179191200-179210400	Strong transcription	Thymus	Thymus
11	chr5:179192000-179193600	Genic enhancers	H9 Derived Neuron Cultured Cells	ES cell derived
12	chr5:179192000-179193600	Genic enhancers	Ganglion Eminence derived primary cultured neurospheres	brain
13	chr5:179192000-179193600	Transcr. at gene 5' and 3'	Foreskin Fibroblast Primary Cells skin02	Skin
14	chr5:179192000-179193800	Genic enhancers	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
15	chr5:179192000-179193800	Genic enhancers	Fetal Adrenal Gland	Adrenal Gland
16	chr5:179192000-179194000	Genic enhancers	Primary hematopoietic stem cells G-CSF-mobilized Male	--
17	chr5:179192000-179194000	Genic enhancers	Foreskin Melanocyte Primary Cells skin01	Skin
18	chr5:179192000-179194400	Genic enhancers	Stomach Smooth Muscle	stomach
19	chr5:179192000-179200000	Genic enhancers	Primary hematopoietic stem cells short term culture	blood
20	chr5:179192000-179202000	Strong transcription	iPS-15b Cell Line	embryonic stem cell
21	chr5:179192000-179207800	Strong transcription	Fetal Thymus	thymus
22	chr5:179192200-179193600	Strong transcription	HUES64 Cell Line	embryonic stem cell
23	chr5:179192200-179193600	Strong transcription	Primary T helper memory cells from peripheral blood 2	blood
24	chr5:179192200-179193600	Strong transcription	Primary T regulatory cells fromperipheralblood	blood
25	chr5:179192200-179193600	Genic enhancers	Fetal Muscle Trunk	muscle
26	chr5:179192200-179193800	Genic enhancers	Brain Inferior Temporal Lobe	brain
27	chr5:179192200-179194000	Genic enhancers	Brain Substantia Nigra	brain
28	chr5:179192200-179194000	Strong transcription	Colonic Mucosa	Colon
29	chr5:179192200-179194400	Genic enhancers	A549	lung
30	chr5:179192200-179194600	Strong transcription	Primary T helper memory cells from peripheral blood 1	blood
31	chr5:179192200-179194800	Strong transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
32	chr5:179192200-179194800	Genic enhancers	Brain Dorsolateral Prefrontal Cortex	brain
33	chr5:179192200-179194800	Strong transcription	Fetal Kidney	kidney
34	chr5:179192200-179195600	Genic enhancers	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
35	chr5:179192200-179200000	Genic enhancers	Primary neutrophils fromperipheralblood	blood
36	chr5:179192200-179206200	Strong transcription	HUES48 Cell Line	embryonic stem cell
37	chr5:179192200-179206200	Strong transcription	Primary B cells from peripheral blood	blood
38	chr5:179192200-179206400	Strong transcription	Primary T helper 17 cells PMA-I stimulated	--
39	chr5:179192200-179206400	Strong transcription	HepG2	liver
40	chr5:179192200-179207600	Strong transcription	Fetal Lung	lung
41	chr5:179192200-179207800	Strong transcription	Primary T helper cells fromperipheralblood	blood
42	chr5:179192200-179208000	Strong transcription	iPS-18 Cell Line	embryonic stem cell
43	chr5:179192200-179210400	Strong transcription	Brain Germinal Matrix	brain
44	chr5:179192400-179193600	Genic enhancers	Placenta	Placenta
45	chr5:179192400-179193800	Genic enhancers	HUES6 Cell Line	embryonic stem cell
46	chr5:179192400-179193800	Genic enhancers	IMR90 fetal lung fibroblasts Cell Line	lung
47	chr5:179192400-179193800	Genic enhancers	Breast Myoepithelial Primary Cells	Breast
48	chr5:179192400-179193800	Transcr. at gene 5' and 3'	Foreskin Fibroblast Primary Cells skin01	Skin
49	chr5:179192400-179193800	Genic enhancers	Brain Cingulate Gyrus	brain
50	chr5:179192400-179193800	Genic enhancers	Brain Hippocampus Middle	brain

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